Genetic Variant :null (chr19-39245644-CATAT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.035 ( 247 hom., cov: 0)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

1 publications found

Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0351

AC:

4818

AN:

137414

Hom.:

247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0153

Gnomad ASJ

AF:

0.00150

Gnomad EAS

AF:

0.00241

Gnomad SAS

AF:

0.000969

Gnomad FIN

AF:

0.0112

Gnomad MID

AF:

0.0101

Gnomad NFE

AF:

0.00500

Gnomad OTH

AF:

0.0274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0351

AC:

4830

AN:

137468

Hom.:

247

Cov.:

AF XY:

0.0349

AC XY:

2302

AN XY:

65946

show subpopulations

African (AFR)

AF:

0.111

AC:

4143

AN:

37240

American (AMR)

AF:

0.0153

AC:

204

AN:

13322

Ashkenazi Jewish (ASJ)

AF:

0.00150

AC:

AN:

3344

East Asian (EAS)

AF:

0.00264

AC:

AN:

4554

South Asian (SAS)

AF:

0.000973

AC:

AN:

4110

European-Finnish (FIN)

AF:

0.0112

AC:

AN:

7614

Middle Eastern (MID)

AF:

0.0111

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.00500

AC:

321

AN:

64248

Other (OTH)

AF:

0.0278

AC:

AN:

1908

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

187

374

560

747

934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0107

Hom.:

677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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19-39245644-CATATATATATATATATAT-CATATATATATATAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over